allmaxdist              Calculates maxdist for all pairs of taxa in a
                        phylogeny.
ancestrallineages       Extracts lineages leading to two tips, t1 and
                        t2, from their most recent common ancestor.
calcConv                Quantifies convergent evolution by the ratio of
                        the current to maximum past phenotypic distance
                        between two or more lineages, as described in
                        Stayton (2015). Code written by Jonathan S.
                        Mitchell for Zelditch et al. (2017).
calcConvCt              Computes Ct-metric scores for putatively
                        convergent tips (or groups of tips) given a set
                        of user provided phenotypic characters and a
                        time calibrated phylogeny.
calcCs                  Calculates the C1-C4 measures of convergent
                        evolution between two lineages as described in
                        Stayton (2015). All measures quantify
                        convergence by the ratio of current to maximum
                        past phenotypic distance between lineages. Can
                        be used as-is but more often will be used
                        within the calcConv script. Code written by
                        Jonathan S. Mitchell for Zelditch et al. (2017)
calcCsCt                Computes Ct values for a pair of tips.
                        Internal, called in calcConv.
calcchanges             Calculates all phenotypic changes that occur on
                        all branches of a phylogeny.
convSig                 Uses simulations to assess the significance of
                        C1-C4 measures of convergent evolution as
                        described in Stayton (2015). Code written by
                        Jonathan S. Mitchell for Zelditch et al. (2017)
convSigCt               Computes and conducts significance tests on
                        Ct-metric scores for putatively convergent tips
                        (or groups of tips) given a set of user
                        provided phenotypic characters and a time
                        calibrated phylogeny.
convnum                 Quantify convergence by the number of
                        convergent events
convnumsig              Assess the significance of convergent evolution
                        using simulations and the convnum metric
convrat                 Quantifies convergent evolution using the C1,
                        C2, C3, and C4 measures as described by Stayton
                        (2015).
convratsig              Tests the signifiance of convergent evolution
                        by the ratio of the current to maximum past
                        phenotypic distance
findanc                 Find the ancestor of a given node in a
                        phylogeny
labelstonumbers         Converts taxon names to tip/edge numbers
maxdist                 Calculates the maximum phenotypic distance
                        between the lineages leading to a pair of taxa.
multianc                Reconstructs ancestral states for multiple
                        characters
phy                     Sample phylogeny for use in convevol examples
                        and tutorial
plot2D                  Plots calcConv or convSig output as a
                        two-dimensional time series.
plotCt                  Plots calcConv or convSig output.
plotellipse             Plots an ellipse
pullNodeSeq             Extracts a vector of ancestors for a given
                        taxon. Code written by Jonathan S. Mitchell for
                        Zelditch et al. (2017)
pwCheck                 Calculates the number of measurements that can
                        be made between two lineages for each pairwise
                        comparison within a set of putatively
                        convergent tips (group identity may also be
                        taken into account). Useful for determining
                        which comparisons are not informative, and
                        constructing a group object before running
                        calcConvCt or convSigCt.
trait                   Sample data for use in convevol examples and
                        tutorial
